bioinformatics
Projects with this topic
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auxiliary tools for bioinformatic pipelines and sequencing data manipulation
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Environment-dependent evolution of digital organisms simulator.
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DuploMap is designed to improve precision and recall of long-read alignments in segmental duplications.
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A tree-based orthology inference program with additional functionality for reducing contamination.
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Lectures by Sven Rahmann in the form of Jupyter notebooks
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[mirror] BAM file annotation with mutations.
This is just a mirror. Head over to Codeberg.org for active development
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Fungal Secreted Proteins (or Secretome) Predictor Pipeline
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OTP, One Touch Pipeline, Documentation at https://one-touch-pipeline.gitlab.io/otp/
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Snakemake RNAseq processing pipeline (STAR or Salmon) via a SLURM cluster
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Crawl any filesystem for genome data, providing one-click opening in IGV
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Fungal Secreted Proteins (or Secretome) Annotation Pipeline
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Python scripting for molecular dynamics simulation using GROMACS
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CommunityYeastract database and web php front-end
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A Swiss Knife suite to manage pipeline environments
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Unix toolkit for feature analysis of alternative splicing events. Includes basic functions for manipulating tables, extraction of exon and intron-related features, discriminate feature analysis, motif maps for RNA-binding proteins, and more.
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Alignment search tool that identifies similar proteomes
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This project includes python scripts with examples used for the below article in GBE. It is also archived on Figshare (https://doi.org/10.6084/m9.figshare.17111693).
Red algal plastids exhibit large genome size variation, especially in the recently described subphylum Proteorhodophytina. By contrast, their mitochondrial genomes remain unexplored. Here, we sequenced, assembled, and analyzed new plastid and mitochondrial genomes of 25 species of red microalgae. We uncovered new cases of genome size expansion in plastids and mitochondria, in both cases associated with group II intron proliferation. The phylogenomic analysis supported that these expansions occurred several times independently. URL: https://doi.org/10.1093/gbe/evac037
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